Forest plot individual gene from 2x3 factor analysis

Forest plot individual gene from 2x3 factor analysis using either base graphics, plotly or ggplot2.

forest_plot(
  object,
  genes,
  scheme = c("red", "green3", "blue"),
  labs = NULL,
  error_type = c("ci", "se"),
  error_width = 0.05,
  gap = 1,
  transpose = FALSE,
  mar = if (transpose) c(5, 7, 5, 4) else c(5, 5, 5, 3),
  ...
)

forest_plotly(
  object,
  genes,
  scheme = c("red", "green3", "blue"),
  labs = NULL,
  error_type = c("ci", "se"),
  error_width = 4,
  gap = 1,
  transpose = FALSE,
  ...
)

forest_ggplot(
  object,
  genes,
  scheme = c("red", "green3", "blue"),
  labs = NULL,
  error_type = c("ci", "se"),
  error_width = 0.3,
  facet = TRUE,
  gap = 1,
  transpose = FALSE,
  ...
)

Arguments

object	A 'volc3d' class object from a 2x3 analysis generated by deseq_2x3_polar()
genes	Vector of genes to plot
scheme	Vector of 3 colours for plotting
labs	Optional character vector of labels for the groups
error_type	Either "ci" or "se" to specify whether error bars use 95% confidence intervals or standard error
error_width	Width of error bars
gap	Size of gap between groupings for each gene
transpose	Logical whether to transpose the plot
mar	Vector of margins on four sides. See par()
...	Optional arguments
facet	Logical whether to use facets for individual genes (ggplot2 only)

Value

Returns a plot using either base graphics (forest_plot), plotly (forest_plotly) or ggplot2 (forest_ggplot). forest_plot also invisibly returns the dataframe used for plotting.

See also

deseq_2x3_polar()